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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagagttttggaacccgcccttctgttttttattcgaatgaagcttttcggtagtgttctttgaaagctaacttctagacatgaatgttttacacttttgcagTCATCATATGGATTTGTTCACTACTTTGATCGAAGATGTGCTAGTATGGCTATAATGACTCTTAACGGAAGGCATAT

Basic information

species Arabidopsis thaliana
transcript AT1G54080.2
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G54080.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA07G04640.1 (Glycine max), 3'ss of exon 3
gtagagttttgga---acccgcccttctgttttttattcgaatgaagcttttcggtagtgttctttgaaagctaacttctagacatga-atgttttacac---ttttgcagTCATCATATGGATTTGTTCACTACTTTGATCGAAGATGTGCTAGTATGGCTATAATGACTCTTAACGGAAGGCATAT
||| | ||||      |     |  | ||| |  | |   |||  |  ||||    | |      |||||    |  | || |  ||| || |  | |     ||||||||||||| ||||||||  |||| ||||||||||| |||| ||||  | | || ||| |  |||| || ||||||||| |
gtatatttttttgcttagttatctctttgtctaatttcttaatttaaattttaaagactagc---tgaaaatggagctttatatttgacatttggtgcctttgttttgcagTCATCCTATGGATTCATTCATTACTTTGATCGCAGATCTGCTGCTCTTGCCATATTATCTCTCAATGGAAGGCATCT

upper sequence: AT1G54080.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA16G01230.1 (Glycine max), 3'ss of exon 3
----gtagagttttgg--aacccgcccttctgttttttattcgaatgaagcttttcggtagtgttctttgaaagctaacttctagacatga-at---gttttacacttttgcagTCATCATATGGATTTGTTCACTACTTTGATCGAAGATGTGCTAGTATGGCTATAATGACTCTTAACGGAAGGCATAT
     |    |||| |  ||        | ||| |  | |   |||  |  ||||    | |  |   | ||||   |  | || |  ||| ||   || |     ||||||||||||| ||||||||  |||| ||||||||||| |||| ||||  | | || ||| |  |||| || ||||||||| |
gtatatctttttttagctaagttatgtctttgtctaatttgttaatttaaattttaaaaactagt---taaaagtggagctttatatttgacatttggtgtctttgttttgcagTCATCCTATGGATTCATTCATTACTTTGATCGCAGATCTGCTGCTCTTGCCATATTATCTCTCAATGGAAGGCATCT

upper sequence: AT1G54080.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv09s0002g00880.t01 (Vitis vinifera), 3'ss of exon 3
-----------------------------------------------------gtagagttttg-gaacccgcccttctgttttttattcg--aatgaagcttt---tcggtagtgttctttgaaagctaacttctagacatg---aatgttttacacttttgcagTCATCATATGGATTTGTTCACTACTTTGATCGAAGATGTGCTAGTATGGCTATAATGACTCTTAACGGAAGGCATAT
                                                     | |||  | |  | |   |   ||    || | |   |  | |  ||| ||   ||  |    ||  | |      | | | | |||||    | || ||  |     |||||||||| ||||||||  | |||||||||||||| |||| ||||    |||||||| || |||| |||||||||||| |
gtatattcttctttatgctatcttgttaatttttggattgtacctgttaagctgaagatctgtatggaaaagttattagacttctcacatgttagtttagcattctatcccttactttgctggtttatcatcatattgacatctccattgattctcctcggtgcagTCATCCTATGGATTCATCCACTACTTTGATCGCAGATCTGCTGCATTGGCTATATTGTCTCTAAACGGAAGGCATCT

upper sequence: AT1G54080.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: PP1S84_50V6.1 (Physcomitrella patens), 3'ss of exon 4
gtagagttttggaacccgcccttctgttttttattcgaatgaagcttt----tcggtagtgtt-ctttgaaagctaacttctagacatgaatgttttacacttttgcagTCATCATATGGATTTGTTCACTACTTTGATCGAAGATGTGCTAGTATGGCTATAATGACTCTTAACGGAAGGCATAT
      |||        |    |     || || |  || |||| |||    ||  | | ||  | |||     | |    |      |  | ||||    | |||||||||||||||||||||||| ||||||| || |  |  | ||||    | ||  |||  ||||| || || || |  ||
------tttaactgaatgtttcttgacattatactttaaggaagttttcaattctttcgagtcgcattggggtttgatagttcatttcgtgtttttt---ttcttgcagTCATCATATGGATTTGTTGACTACTTGGACCATATTTATGCTGCAGTAGCATTAACTACTCTAAATGGCAGACTAAT

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|124847638|gb|EH932075.1|EH932075
EST:     TTGCAAGTACTGGTCCTATTGAAAGCTGTAAACTCATCAGAAAGGATAAG                         TCATCATATGGATTTGTTCACTACTTTGATCGAAGAT
genomic: TTGCAAGTACTGGTCCTATTGAAAGCTGTAAACTCATCAGAAAGGATAAGgtagagtttt ... acttttgcagTCATCATATGGATTTGTTCACTACTTTGATCGAAGAT
EST: gi|125255088|gb|EL269173.1|EL269173
EST:     TTGCAAGTACTGGTCCTATTGAAAGCTGTAAACTCATCAGAAAGGATAAG                         TCATCATATGGAT
genomic: TTGCAAGTACTGGTCCTATTGAAAGCTGTAAACTCATCAGAAAGGATAAGgtagagtttt ... acttttgcagTCATCATATGGAT
EST: gi|164208889|gb|ES026100.1|ES026100
EST:     TCCTATTGAAAGCTGTAAACTCATCAGAAAGGATAAG                         TCATCATATGGATTTGTTCACTACTTTGATCGAAGATGTGCTAGTATGGCT
genomic: TCCTATTGAAAGCTGTAAACTCATCAGAAAGGATAAGgtagagtttt ... acttttgcagTCATCATATGGATTTGTTCACTACTTTGATCGAAGATGTGCTAGTATGGCT
EST: gi|125239302|gb|EL253387.1|EL253387
EST:     TTGCAAGTACTGGTCCTATTGAAAGCTGTAAACTCATCAGAAAGGATAAG                         TCATCATATGGATTTGTTCACTACT
genomic: TTGCAAGTACTGGTCCTATTGAAAGCTGTAAACTCATCAGAAAGGATAAGgtagagtttt ... acttttgcagTCATCATATGGATTTGTTCACTACT
EST: gi|125262858|gb|EL276943.1|EL276943
EST:     TGCAAGTACTGGTCCTATTGAAAGCTGTAAACTCATCAAGAAAGGATAAG                         TCATCATATGGAT
genomic: TGCAAGTACTGGTCCTATTGAAAGCTGTAAACTCATCA-GAAAGGATAAGgtagagtttt ... acttttgcagTCATCATATGGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cggtagtgttctttgaaagctaacttctagacatgaatgttttacacttttgcagTCATCATATGGATTTGTTCACTACTTTGATCGAAGATGTGCTAGTATGGCTATAATGACTCTTAACGGAAGGCATAT
                 agctaac  putative branch site (score: 2)
                                            cactttt  putative PPT
                                   aatgtttta  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtagagttttggaacccgcccttctgttttttattcgaatgaagcttttcggtagtgttctttgaaagctaacttctagacatgaatgttttacacttttgcagTCATCATATGGATTTGTTCACTACTTTGATCGAAGATGTGCTAGTATGGCTATAATGACTCTTAACGGAAGGCATAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG